From 13aa2951c14f63ed67d5ac4b66f0327c4efeae16 Mon Sep 17 00:00:00 2001
From: xuewei cao <36172337+xueweic@users.noreply.github.com>
Date: Wed, 26 Mar 2025 18:16:56 -0400
Subject: [PATCH] minor fix

minor fix if region does not have sumstats variants
---
 R/colocboost_pipeline.R |  1 +
 R/file_utils.R          | 10 ++++++++++
 R/univariate_pipeline.R |  7 ++++++-
 3 files changed, 17 insertions(+), 1 deletion(-)

diff --git a/R/colocboost_pipeline.R b/R/colocboost_pipeline.R
index e5d8f8b1..65d2053d 100644
--- a/R/colocboost_pipeline.R
+++ b/R/colocboost_pipeline.R
@@ -680,6 +680,7 @@ qc_regional_data <- function(region_data,
       sumstats <- sumstat_data$sumstats[[i]]
       for (ii in 1:length(sumstats)) {
         sumstat <- sumstats[[ii]]
+        if (nrow(sumstat$sumstats) == 0) next
         n <- sumstat$n
         var_y <- sumstat$var_y
         conditions_sumstat <- names(sumstats)[ii]
diff --git a/R/file_utils.R b/R/file_utils.R
index 47b82ea5..f0c8ce1e 100644
--- a/R/file_utils.R
+++ b/R/file_utils.R
@@ -799,6 +799,16 @@ load_rss_data <- function(sumstat_path, column_file_path, n_sample = 0, n_case =
   sumstats <- NULL
   var_y <- NULL
   sumstats <- load_tsv_region(file_path = sumstat_path, region = region, extract_region_name = extract_region_name, region_name_col = region_name_col)
+  
+  # To keep a log message
+  n_variants <- nrow(sumstats)
+  if (n_variants == 0){
+      message(paste0("No variants in region ", region, "."))
+      return(list(sumstats = sumstats, n = NULL, var_y = NULL))
+  } else {
+      message(paste0("Region ", region, " include ", n_variants, " in input sumstats."))
+  }
+  
   # Standardize column names based on mapping
   for (name in colnames(sumstats)) {
     if (name %in% column_data$original) {
diff --git a/R/univariate_pipeline.R b/R/univariate_pipeline.R
index e07bb07b..a80ba03c 100644
--- a/R/univariate_pipeline.R
+++ b/R/univariate_pipeline.R
@@ -195,6 +195,11 @@ rss_analysis_pipeline <- function(
   sumstats <- rss_input$sumstats
   n <- rss_input$n
   var_y <- rss_input$var_y
+    
+  # Check if no variants in sumstats
+  if (nrow(sumstats)==0){
+      return(list(rss_data_analyzed = sumstats))
+  }
 
   # Preprocess the input data
   preprocess_results <- rss_basic_qc(sumstats, LD_data, skip_region = skip_region, remove_indels = remove_indels)
@@ -204,7 +209,7 @@ rss_analysis_pipeline <- function(
   if (pip_cutoff_to_skip != 0) {
     if (pip_cutoff_to_skip < 0) {
       # automatically determine the cutoff to use
-      pip_cutoff_to_skip <- 3 * 1 / ncol(X)
+      pip_cutoff_to_skip <- 3 * 1 / nrow(sumstats)
     }
     top_model_pip <- susie_rss_wrapper(z = sumstats$z, R = LD_mat, L = 1, n = n, var_y = var_y)$pip
     if (!any(top_model_pip > pip_cutoff_to_skip)) {